We have sequenced a chloroplast genome approximately 150kbp. We did about 100k 454 Titanium reads for approximately 30 million bases and 200x depth. However, when we run the assembly on Newbler (default parameters) we get roughly 10k contigs, the largest contig size is ~15kbp. My questions are:
1. What can we do to improve this assembly? What are the typical steps in this kind of situation?
2. Are these results typical? With this kind of depth, we were expecting a complete, or nearly complete, assembly result.
Thanks very much in advance for your help.
1. What can we do to improve this assembly? What are the typical steps in this kind of situation?
2. Are these results typical? With this kind of depth, we were expecting a complete, or nearly complete, assembly result.
Thanks very much in advance for your help.
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